Skip to content

0.a Installation

Jump to bottom
Qingqing Wang edited this page Apr 10, 2023 · 19 revisions

Requirements:

  • Perl (5+) with modules Array::Utils and Statistics::Descriptive (for checking if modules are already installed and instructions of installing perl modules see Additional Installation Tips below)
  • Samtools (1.3.1+)
  • Bedtools (2.26.0+)
  • R version 3+ (See Additional Notes below for users that have no root access to R on a shared computer cluster)
  • The Bioconductor package in R (https://www.bioconductor.org/install/)
  • The DEXSeq package in R (https://bioconductor.org/packages/release/bioc/html/DEXSeq.html)
  • STAR (2.5.x+)

Make sure that these can be directly executed through your PATH.

Installation:

Additional Notes

  • JUM exclusively uses RNA-seq reads mapped to splice junctions to construct statistical models and quantify AS changes, therefore the depth of RNA-seq datasets affects how many alternative splicing (AS) events will be found. We have successfully used Drosophila samples of as low as ~20M reads and human samples of as low as ~35M reads to detect hundreds to thousands of significantly changed AS events.
  • JUM uses biological replicates to build statistical models. Ideally for each condition the user will have >= 2 replicates. If not, refer to https://github.com/qqwang-berkeley/JUM/wiki/4.2.-Workaround-if-you-do-not-have-biological-replicates-(version-2.0.2-) for a workaround.
  • For users that use shared computer clusters: In general the default directory to install additional R packages is restricted to the admin. Users need to initiate R to install packages in a customer directory. To do that, start R and execute the following commands (here we use the package DEXSeq as an example. Users can use any R packages). R would automatically ask and confirm a customer directory to install R packages and this only needs to be done once. For earlier R versions: 
    $ R
> source("http://bioconductor.org/biocLite.R")
> biocLite("DEXSeq", dependencies=TRUE)
    For R v4+: 
    $ R
> if (!require("BiocManager", quietly = TRUE))
> install.packages("BiocManager")
> BiocManager::install(version = "3.16")
> BiocManager::install("DEXSeq")
  • For more questions about R (version compatibility etc.) and troubleshooting check this FAQ page here.

Additional Installation Tips

  • To check if a perl module is already installed, do the following:
$ perl -e 'use Statistics::Descriptive;'
$ perl -e 'use Array::Utils;'

There should be no message from Linux if the modules are already installed.

  • To install perl module using CPAN on a server without root access, do the following (assuming your linux system profile is named .profile, you may need to change that to be .bash_profile, .bashrc, etc.):
$ wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib
$ eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`
$ echo 'eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`' >> ~/.profile
$ echo 'export MANPATH=$HOME/perl5/man:$MANPATH' >> ~/.profile
  • To configure CPAN:
$ cpan
  > Would you like to configure as much as possible automatically? [yes] 
  > yes
  > What approach do you want?  (Choose 'local::lib', 'sudo' or 'manual')
  > [local::lib] local::lib
  > Would you like me to append that to /user/home/.bashrc now? [yes] 
  > yes
  > exit
  • To install a perl module do:
$ cpanm Module::Name

For example, to install the two modules that JUM needs:

$ cpanm Array::Utils 
$ cpanm Statistics::Descriptive
Clone this wiki locally